Hi, Salameh, As Pavel said, you might have a ligand with incorrect cif file. A quick fix is to run phenix.elbow on that cif file, which worked for me. I will try the new version of phenix and to see if it can fix the problem. Hopefully you already solved the problem.
Nian Huang, Ph.D. UT Southwestern Medical Center On Mon, Mar 15, 2010 at 9:14 AM, Salameh, Mohd A., Ph.D. <[email protected]> wrote: > In fact I'm using an older version of phenix 1.26b and never faced a problem, > and worked beautifully on twinned data. do you suggest to upgrade it to the > latest version? Thanks Huang, M > > ********************************** > Mohd A. Salameh, Ph.D. > Mayo Clinic Cancer Center > Griffin Cancer Research building,Rm 331 > 4500 San Pablo Rd > Jacksonville, FL 32224 > Tel: (904) 953-0046 > Fax: (904) 953-0277 > [email protected] > ********************************** > -----Original Message----- > From: Nian Huang [mailto:[email protected]] > Sent: Friday, March 12, 2010 5:49 PM > To: Salameh, Mohd A., Ph.D. > Cc: [email protected] > Subject: Re: [ccp4bb] phenix target weight refinement > > Which version did you use? I remember the old version of phenix (1.3) > will automatically change your setting (wxc and wxu) each round. And > v1.5 will automatically choose wxu if you use tls. I haven't tried 1.6 > yet. Maybe there are some bugs associated with it? > The default wxc is 0.5 and wxu is 1. So the default has tighter weight > than your specification. Just use default setting instead. > > Nian Huang, Ph.D. > UT Southwestern Medical Center > > > On Fri, Mar 12, 2010 at 11:59 AM, Salameh, Mohd A., Ph.D. > <[email protected]> wrote: >> Yes Im using wxc_scale and wxu_scale but I also use tls refinement,so in >> this case if the weights need to be tightly restrained, I should not use >> tls refinement! >> >> ********************************** >> Mohd A. Salameh, Ph.D. >> Mayo Clinic Cancer Center >> Griffin Cancer Research building,Rm 331 >> 4500 San Pablo Rd >> Jacksonville, FL 32224 >> Tel: (904) 953-0046 >> Fax: (904) 953-0277 >> [email protected] >> ********************************** >> >> -----Original Message----- >> From: Phil Jeffrey [mailto:[email protected]] >> Sent: Friday, March 12, 2010 12:37 PM >> To: Salameh, Mohd A., Ph.D. >> Subject: Re: [ccp4bb] phenix target weight refinement >> >> Use wxc_scale and wxu_scale not wxc and wxu. >> If you're doing TLS it will ignore wxu_scale either way. >> >> >> Salameh, Mohd A., Ph.D. wrote: >>> *Dear All,* >>> >>> *In every** refinement** round** the** wxc and wcu** are out of >> control, >>> although I modify the def file and** change the values** ** of** >> wxc=1 >>> and wxu=1** so they are tightly restrained**, but it fail**ed** to** >>> fix the problem,** wxc and wxu** values**** keep fluctuating,**** in >> my >>> latest** refinement** round wxc=256!!** wxu=3. The** Stereochemistry >>> looks** very** loosely restrained** and the** gap between R-free and >>> R-work** is** too big**. I**'**ve been using phenix for almost 4 years >> >>> and** never had this problem,** or once** I** set the values of wxc >> and >>> wxu that will be it, never change.** I** also tried to fix wxc from >> the >>> command line and** didn't** work either (phenix.**refine refine.def >>> fix_wxc=1.0).**** I** will certainly** appreciate** any help**. >> Thanks, >>> Mohd**** ** * >>> >>> ****************************************** >>> >>> *****Mohd A. Salameh, Ph.D.* >>> >>> Mayo Clinic Cancer Center >>> >>> Griffin Cancer Research building,Rm 331 >>> >>> 4500 San Pablo Rd >>> >>> Jacksonville, FL 32224 >>> >>> Tel: (904) 953-0046 >>> >>> Fax: (904) 953-0277 >>> >>> [email protected] >>> >>> **************************************** >>> >> >
